Academic Sequencing Centers May Feel the Pinch of Budgetary Constraints and Data Deluge

NHGRI renewed $416 million over four years in funding for three centers but warned of lower funds in the future.

While the cost of generating a whole genome sequence is dropping, other expenses related to conducting such research, evaluating the data, and using that information persist. [AlienForce - Fotolia.com]

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The cost of sequencing a human genome is approaching the much-noted $1,000 mark and could well arrive by year’s end. This achievement could mean a quicker uptake of sequencing in the clinical setting.

Currently large-scale centers that have cropped up around the country handle the bulk of sequencing activity. While NHGRI renewed $416 million over four years in funding last December for the nation’s three largest genome sequencing centers—Baylor College of Medicine, The Broad Institute, and Washington University in St. Louis—the institute included a warning in its official announcement: “NHGRI plans a gradual reduction in the base funding for the large-scale centers over the next several years as the cost of sequencing continues to drop. The savings will be repurposed as new research opportunities arise.”

While the cost of generating a whole genome sequence is certainly dropping at a rate that seems to be faster than Moore’s Law, several other expenses related to conducting such research, evaluating the data, and using that information persist.

BCM’s Human Genome Sequencing Center

Baylor College of Medicine (BCM) faces an approximately 12% reduction in its overall budget because of reduced federal funding. NHGRI did, however, come through on two major grants announced in December: $85.2 million for BCM’s Human Genome Sequencing Center (HGSC), and $16 million toward a collaboration between BCM and Johns Hopkins University School of Medicine.

The money for HGSC is a renewal and spans four years. It covers about 80% of HGSC’s funding and will support research with other NHGRI-funded large-scale genome centers including the Genome Institute at Washington University in St. Louis and the Broad Institute of MIT and Harvard.

The grant awarded to the Baylor-Johns Hopkins partnership also spans four years. It will be used to create a center focused on studying the cause of Mendelian disorders. The researchers will work toward improving the technology involved in studying these diseases through “better, less costly exome screening and improved variant calling,” spokeswoman Glenna Picton told GEN.

Other priorities at BCM include research into cancer and common diseases as well as the expansion of its data management resource to handle the deluge of data. Its sequencing equipment includes 15 HiSeqs from Illumina, 10 sequencers from Roche, as well as 12 ABI SOLiDs, five ABI 3730s, and four Ion Torrents from Life Technologies. It was yet to be determined at deadline whether any equipment would be added or subtracted this year.

Cold Spring Harbor Laboratory

Cold Spring Harbor Laboratory (CSHL) operated last year on a budget of $143 million, up from $137 million a year earlier. Commenting on the ubiquitousness of sequencing research at CSHL, David L. Spector, Ph.D., director, research and professor at CSHL, told GEN, “We have 50 principal investigators, and I think it’s fair to say that virtually every investigator is doing some level of sequencing. It’s becoming more of a general tool for everyone, whether they’re working in cancer or neuroscience or plant biology, whether their questions are relating directly to sequence analysis or epigenetic marks or methylation.”

Dr. Spector said CSHL is seeking a founding program chair for its Simons Center for Quantitative Biology: “Once that individual is on board, we will likely hire an additional three faculty probably.” Two PIs will also be brought on board for CSHL’s cancer therapeutic effort, with several existing investigators planning to move research projects in that direction. “This will put us in a transition proposition, from doing basic science to moving it more toward a clinical setting,” Dr. Spector said. “There will certainly be an aspect involving sequencing approaches.”

Dr. Spector pointed to the New York Genome Center (NYGC), saying, “This will give us expanded capabilities for sequencing and also will provide us with accessibility to a CLIA lab should our scientists start working with clinical samples and needing to examine them in a more defined way.” CSHL is a founding member of NYGC.

W. Richard McCombie, Ph.D., offered an illustration of how the data deluge is driven by sequencing: “My lab just submitted a purchase order for about a half-million dollars for disk drives during the last week of December,” Dr. McCombie told GEN. “The lab will be spending several million dollars—between $2 million and $3 million—in the upcoming year for upgrades to computer infrastructure and storage.

“We have a committee in the lab that’s looking at various long-term options including cloud storage.” Dr. McCombie said that at present, his lab carries out tiered storage. Higher speed, more expensive storage is used for data that requires rapid disk throughput, and lower-cost storage is used for data it does not access as much.

Institute for Genome Sciences

The Institute for Genome Sciences (IGS) expects its 2012 budget to stay flat at last year’s $30 million level. Of that total, $18 million came from grants and contracts secured by researchers, while the rest came from seed funding and other sources. IGS generated $3.5 million of its revenue from its core lab, with industry accounting for about 10% of that revenue, Lori McKay, IGS senior administrator, told GEN.

After four to five years of rapid growth, “we will continue to go up, but it will be incrementally,” McKay continued. “I don’t see anything coming down the pike that would increase our revenues substantially.”

In terms of research focus, Luke J. Tallon, scientific director of the Genomics Resource Center at IGS, told GEN, “we’re going down a couple of different paths. One is looking more at host-pathogen interaction. So we’ve done a lot of sequencing of human pathogens, both bacterial and viral and parasitic. But we’re now starting to look much more at the human hosts, and how genetic variations and things can affect infectious diseases and the outcomes.

“And then we’re also looking at diseases that are not infectious, things like cancer or other conditions that are not the result of a pathogen, and how host variation can play a role in the outcome of those.”

IGS plans on upgrading its sequencing equipment. The institute recently decommissioned its Illumina Genome Analyzer sequencers, bought a second Illumina HiSeq, invested in Illumina’s MiSeq, and is carrying out beta testing of Pacific Biosciences’ RS sequencing system. IGS was among several institutions to beta test the C2 upgrade to the RS system. C2 consists of new chemistry, enhanced nanofabricated consumable substrates, and improved software.

The institute will add to its 22 PIs by hiring two new faculty members in 2012. Each, in turn, will bring to IGS their own assistants. “I would say we will probably increase this year by about 10 employees,” McKay noted.

The Centre for Applied Genomics

The Centre for Applied Genomics (TCAG) expects a 20% bump to its 2012 budget. Final 2011 figures were unavailable, though in 2010 TCAG had an overall budget of $20.8 million. Its budget has been growing at a 20% average rate for the past five years. “We thus expect that the 2011 and 2012 budgets will grow by this amount, mainly due to the initiation of a number of large-scale projects using the facility’s services and incremental growth to our client-based service work,” spokeswoman Suzanne Gold told GEN.

Some 60% of TCAG’s total budget consists of billings from fee-for-service experimentation and data analysis for hundreds of academic, government, nongovernmental organizations, and private sector scientists. Academic researchers are by far the largest group, accounting for about 92% of clients.

TCAG funding comes primarily from its parent institution, The Hospital for Sick Children (SickKids) Research Institute, SickKids Foundation, as well as from Genome Canada, the Ontario Ministry of Economic Development and Innovation, and the Canada Foundation for Innovation. SickKids is building at $400 million Research & Learning Tower, of which TCAG will occupy a full floor (roughly 30,000 square feet) beginning in late 2013. However, TCAG will have sooner access to the tower’s new data center and high-performance computing facility, which are expected to come online in April 2013.

Even with diminished government dollars, especially from deficit-addled Washington, sequencing centers can still expect to grow in coming years since the need for sequencing is not going to disappear. Centers that have relied heavily on government dollars may consider shifting toward generating revenue through sequencing services, an approach that has worked for TCAG thus far.

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